I've always wondered how many actors ever made up a system for themselves as suggested in "Galaxy Quest" as opposed to those who just pushed random buttons on their shiny control systems. Very few fans will ever notice but I have always wondered and never really observed which they use.
Based on Klingon Academy, the last Star Trek sim I ever bought, I have to assume that I can fly any ship with my computer joystick handling firing, speed, and steering wether its a glorified shuttle or a battleship.